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Class 3 Asparaginases

Class Overview

6 experimentally studied proteins

0 sequences in Swiss-Prot

18,698 unique sequences in UniRef100

Bacteria (and fungi)

Affinities to l‑asparagine and sometimes l‑glutamine

Dimeric and possibly monomeric structures

Reference Monomer1

Reference Structure

Clan 1 Clan 2 Clan 3 Clan 4
Family 1 Bacterial asparaginases with minimal glutaminase activity. Family 2 Potentially high affinity extracellular asparaginases from actinomycetota bacteria. Family 3 Contains the dimeric Rhizobium etli "type V" asparaginase. Family 4 Contains the dimeric Rhizobium etli "type IV" asparaginase.

Experimentally Studied Proteins

Fam ? Class - Clan - Family Alt ? Alternative historical name / classification AN ? UniProt accession number Name ? UniProt entry name, only given here for Swiss-Prot entries EC Organism Cell-Loc AAs Structure PDB Km i for Asn [mM] Vmax i for Asn [μmol/min/mg] Kcat i for Asn [s-1]
3-1-1 - A0A0C5GVW3 3.5.1.1 Paenibacillus barengoltzii - 336 Monomer i Determined by gel filtration. - 3.6 162.2 -
3-1-1 - A0A068N0Z8 3.5.1.1 Synechocystis sp. - 317 - - 29 25.7 -
3-2-2 - W0KM71 3.5.1.1 Nocardiopsis alba Extracellular 320 - - 0.127 5.5 -
3-2-2 - Q54237 3.5.1.1 Streptomyces griseus Extracellular (putative) 328 - - - - -
3-3-3 ReAV Q2K0Z2 3.5.1.1 Rhizobium etli - 367 Homo dimer 7OS6 PDBs 4.2 - 438
3-4-4 ReAIV Q2KB35 3.5.1.1 Rhizobium etli - 335 Homo dimer 8CLZ PDBs 1.34 - 411

Swiss-Prot Sequences

UniRef100 Sequences2

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Phylogenetic Tree and Introduction

Class 3 l‑asparaginases, previously known as Rhizobium etli-type l‑asparaginases, are the smallest and most recently discovered class. Class 3 l‑asparaginases can be found in a range of bacteria, not only in the nitrogen-fixing Rhizobium etli and related bacteria, and some fungi probably due to horizontal gene transfer. It is worth noting a few archaea carrying the gene for a Class 3 l‑asparaginase were identified with BLAST.

Similarly to Class 1 and Class 2, Class 3 l‑asparaginases can show a low sequence identity to each other but the tertiary structure is well conserved in the class. Class 3 l‑asparaginases could hold untapped potential in clinical applications, as some sequences have been shown to have high affinity to l‑asparagine and undetectable l‑glutaminase activity. No Class 3 sequence with other activities could be identified in the literature. Each Class 3 clan only holds one family at the moment.

Phylogenetic tree

Representative Sequence Alignment

Conserved Motifs of Families

Motifs Image

Families Overview

Clan Family UniProt ID: (name, PDB) Activity Extra domains Protein structure Molecular weight Taxonomy Cell location Km (Asn)
1 1 U*: A0A0C5GVW3 U*: A0A068N0Z8 ASNase with minimal GLNase - monomer (putative) ~41 kDa
~34 kDa
bacteria - mM
2 2 U*: W0KM71
U*: Q54237
ASNase - - - bacteria (actinomycetota) extracellular μM
3 3 U*: Q2K0Z2
(ReAV, 7OS6)
U: A0A0A2JT57
ASNase - homo dimer ~47 kDa bacteria and some eukaryotes (fungi) - mM
4 4 U*: Q2KB35
(ReAIV, 8CLZ)
U: A0A109BI20
ASNase - homo dimer - bacteria (mostly pseudomonadota) - mM

Entry: S = Swiss-Prot, U = UniProtKB, P = UniParc, * = experimentally studied protein, UniProt accession number (short protein name, PDB id). Activity: ASNase = l‑asparaginase, GLNase = l‑glutaminase. Molecular weight is for a monomeric unit. Km is for l‑asparagine: μM = Km < 1 mM, mM = Km ≥ 1 mM.


1Varadi, M et al. AlphaFold Protein Structure Database in 2024: providing structure coverage for over 214 million protein sequences. Nucleic Acids Research (2024). Licensed under CC BY 4.0.

2Suzek, B.E. et al. UniRef: comprehensive and non-redundant UniProt reference clusters. Bioinformatics (2007). Licensed under CC BY 4.0. Added classification code to sequence headers.


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